The Brain Connectivity Toolbox (brain-connectivity-toolbox.net) is a MATLAB toolbox for complex-network analysis of structural and functional brain-connectivity data sets.
Complex network measures of brain connectivity: Uses and interpretations.
Rubinov M, Sporns O (2010) NeuroImage 52:1059-69.
The Brain Connectivity Toolbox codebase is widely used by brain-imaging researchers, and has been wholly or partially ported to, or included in, the following projects:
bctpy: Brain Connectivity Toolbox for Python.
bct-cpp: Brain Connectivity Toolbox in C++.
Human Connectome Project: An NIH consortium for mapping brain white-matter pathways.
Virtual Brain Project: A consortium for simulation of primate brain-network dynamics.
FieldTrip: Advanced analysis toolbox of MEG, EEG, and invasive electrophysiological data.
GraphVar: A user-friendly GUI-based toolbox for graph-analyses of brain connectivity.
Network Based Statistic Toolbox: A toolbox for testing hypotheses about the connectome.
Neuroimaging Analysis Kit: A library of modules and pipelines for fMRI processing.
Graph Theory GLM Toolbox: A GLM toolbox of brain-network graph-analysis properties.
Brainnetome Toolkit: A MATLAB GUI toolkit of complex network measures.
BioNeCT: A cohesive platform for analyzing brain network connectivity in EEG recordings.
GRETNA: A toolbox for comprehensive analyses of topology of the brain connectome.
MIBCA: Automated all-in-one connectivity toolbox with batch processing.
GAT/bnets: Graph Analysis Toolbox of functional and structural brain networks.
BASCO: Inter-regional functional connectivity analysis in event-related fMRI data.
MNET: A fully automated all-in-one network analysis toolbox for fMRI and DTI.
EEGNET: A toolbox for analyzing and visualizing M/EEG connectivity.
BRAPH: Brain analysis using graph theory.